There are multiple direct train connections between Berlin and Prague every day (EuroCity). It takes about 4h30 and you won’t need a reservation, but for only €1,50 I would take it anyway.
There is also a direct Eurocity connection between Prague and Vienna which also takes 4h30.
 
Check for timetables:
Germany: http://www.bahn.de/p/view/international/englisch/international_guests.shtml
Czech Republic: www.cd.cz/static/eng
Austria: www.oebb.at/vip8/oebb/en
 

thx joeri
so i can use my eurail pass for these trains yeh? what exactly do the eurail passes cover? probably a stupid question but the eurail site is v confusing?
also, are most reservations for seats in europe about that price (1.5 euro)? coz i heard that reservations on trains in  Italy are very expensive….

Your eurail pass will cover the base fare for virtually every “train” you take in the countries where it’s valid.  If the train requires a reservation or supplement you will have to pay extra for that.  Supplements are very rare, so you’re unlikely to run into those.  Most trains don’t require reservations, but the express trains between major cities often do, so you’re likely to take trains that require reservations at some point unless you make an effort to avoid them.
 
I only reserve a seat if the train requires a reservation or if I need to arrive somewhere at a specific time so can’t just wait an hour for the next train if one is full.  Unless you’re traveling on some sort of busy day (right before a holiday weekend or something) I would not pay for a reservation in winter unless the train requires it.

It’s true most European trains don’t require a reservation (in general only high speed trains and the long routes and nighttrains require one), so your eurail will do fine, but if you do make a reservation you’re sure to have a seat and no standing place. For example, the German ICE trains don’t require a reservation but are most of the time full and you just don’t want to stand or hang around somewhere for a few hours, just to save a few euros.
 
Reservation prices vary, eastern Europe is a lot cheaper than the western countries ofcourse. Italy is just expensive in all ways, so probably the reservation prices are also high, just check before you book.

Hello All,

You comments and recommendations are very informative. I am also looking into going to Prague. However, direct flights into Prague is too expensive so i’m trying to take alternative route there. My plans were to fly into Frankfurt, take the train to Berlin, and then to Prague. Do you think this is the best route? Please let me know if there’s a more efficient and cheaper way to get to Prague. Thanks.

Look for a flight on a low fare European airline from your arrival city (Frankfurt??) to Prague. Use www.whichbudget.com to see which airlines fly which routes and check our “cheap flights” forum for tips.

Is Frankfurt your cheapest/best choice for an arrival city if you’re trying to get to Prague? If you can fly to Munich or Vienna for roughly the same price that would be an easier/faster train connection to Prague.

You cannot change the trains at the border. The borderpoint is just a tariff point, the train does not stop at the actual border at all. Direct trains run bi-hourly. Of course the conductor will be smart enough to understand you have two different tickets for two different countries, many people travel like that.

If you want to be technical – you get into the train Berlin-Prague in Berlin, the train speeds off, the conductor checks your whole journey ticket, then train crews change at station Decin, the first station on the Czech territory. German conductors, the train chief and the driver descend and Czech personnel gets on board. The new crew then checks the travel documents again. Same in the reverse direction, you get onboard in Prague, Czechs check your tickets, then Germans exchange Czechs in Decin and check the papers once again.

I wouldn’t bother.

Frankfurt has a very frequent air connection with Prague. In fact, most people who leave Prague for the world’s major cities, change at Frankfurt. I’d try a plane. Train may be the same price and much more time consuming.

I have 7 days to spend in Europe. My flight lands in Frankfurt and my plan was to spend all 5 days in Prague. After looking at all that Prague has to offer i think two days there might be enough time to do all the things i want to do. Now, i’m thinking about adding an additional city to my trip, possibly Vienna, Austria since it’s nearby Prague (and it’s another great city). Which two cities would you suggest i travel to for the days that i have that will maximize my experience in terms of time efficiency and the beauty of that city?
Another thing i noticed is that train tickets cannot be booked online from Prague to Vienna (something about tariff). Do you know if there are many connections between those two cities either by train or airplane? And which travel method would you recommend i choose for the time and money? Thanks.

I like Prague a lot better than Vienna. I think you need at least 3 days in Prague. Since you’ve already been using the German rail site for schedules (at least that’s where I assume you got the notice that you can’t book that ticket on-line) you already know the answer to this question. It shows the number of connections for each train. There’s roughly one train every other hour with no connections on this route.